CHANGELOG

This document outlines the major changes to the EpiGraphDB platform and research. Please reach out to us for issues, feedbacks, suggestions and collaborations!

Roadmap

March 2021

Graph database and platform v1.0

• Overhaul on the data integration pipeline and rebuild of the graph database.
• Major updates on the following sources:
  • Reactome
  • MR-EvE
• New integrated data sources
  • ClinVar
  • Annotation of EBI GWAS traits to EFO

For specific details please refer to the version 1 changelog.

August 2020

We have submitted EpiGraphDB R package to CRAN. You can now install.packages("epigraphdb") in R to get a stable version of the epigraphdb package.

July 2020

We have submitted the preprint manuscript describing the EpiGraphDB platform to bioRxiv.

April 2020

EpiGraphDB v0.3.0

EpiGraphDB platform is now v0.3.0!

Graph database (API, and R package have been adapted the corresponding changes):

• Changed
  • Gtex node now called Tissue
  • SNP node now called Variant
  • Disease data now supplied by Mondo (https://mondo.monarchinitiative.org/)
• Added
  • Literature nodes expanded and have extra properties from SemMedDB - backwards compatible as v0.2 pubmed_id property still exists
  • SemMedDB data - SemmedTriple, SemmedTerm nodes
  • MELODI literature enrichments
  • Gwas-EFO via NLP
  • Polygenic Risk Scores
  • Ben Neale genetic correlation data
• Removed
  • EKDRD data
  • MeSH data
  • Old EFO relationships
  • In house genetic correlation data (top SNPs)

The web UI (https://epigraphdb.org) has been refactored with a fresh new look.

August 2019

• EpiGraphDB explorer https://epigraphdb.org/explore/
• EpiGraphDB gallery https://epigraphdb.org/gallery/

July 2019

• v0.2 beta release for web application, API, and R package

2018

• Pilot version